Contacts of the strand formed by residues 314 - 320 (chain B) in PDB entry 5N4D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TYR* 3.7 8.5 - - - -
285B ASN* 2.9 41.0 + - - +
287B LEU* 4.2 14.4 - - + -
307B VAL* 3.6 43.5 - - + +
309B GLU 5.5 0.2 - - - -
311B ALA* 5.5 2.6 - - + +
312B ALA* 3.4 31.4 - - + +
313B ASP* 1.3 75.7 + - - +
315B ASN* 1.3 62.3 + - - +
316B ILE 4.4 0.2 - - - -
326B ILE* 3.9 15.7 - - + -
327B LYS 3.5 4.3 - - - -
328B THR* 3.6 21.1 - - - -
330B LEU* 3.4 30.0 - - + +
338B ILE* 4.2 17.0 - - + -
340B ILE* 5.2 2.9 - - + -
349B ILE* 6.3 1.3 - - + -
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Residues in contact with ASN 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ASP* 4.3 4.4 + - - +
276B TYR* 3.6 19.8 + - - -
313B ASP* 4.5 7.2 - - - +
314B TYR* 1.3 75.6 - - - +
316B ILE* 1.3 76.6 + - - +
317B ILE* 4.1 1.8 - - - +
326B ILE* 3.5 4.0 - - - +
327B LYS* 2.8 57.1 + - + +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ASP* 4.5 8.1 - - + +
274B TYR* 3.7 50.0 - - + +
276B TYR* 3.0 30.2 + - + +
287B LEU* 3.7 20.9 - - + -
289B VAL* 6.0 0.2 - - + -
315B ASN* 1.3 84.9 + - - +
317B ILE* 1.3 64.4 + - - +
318B THR* 3.8 17.3 - - - +
324B VAL* 3.6 22.7 - - + -
325B TYR 3.9 4.3 - - - +
326B ILE* 3.6 12.8 - - + -
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ASN* 4.1 2.7 - - - +
316B ILE* 1.3 78.0 - - - +
318B THR* 1.3 62.5 + - + +
325B TYR* 2.8 16.3 + - + +
326B ILE 3.9 1.3 - - - +
327B LYS* 3.7 31.2 - - + +
337B VAL* 3.7 35.9 - - + -
364B VAL* 3.9 33.0 - - + +
365B ASN* 4.4 0.2 - - - -
366B CYS* 3.9 26.5 + - - +
372B PHE* 4.0 20.4 - - + -
411B GLN* 4.7 1.6 - - - +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B SER* 6.4 0.2 - - - -
268B GLU* 5.5 0.9 + - - +
274B TYR* 4.9 0.7 - - - -
316B ILE* 3.8 8.6 - - - +
317B ILE* 1.3 81.7 - - - +
319B ASN* 1.3 76.4 + - - +
320B HIS* 4.4 7.1 - - - +
324B VAL* 3.7 4.0 - - - +
325B TYR* 2.8 38.8 + - + +
366B CYS* 3.9 13.2 - - + -
372B PHE* 3.8 30.1 - - + -
411B GLN* 2.6 31.2 + - - -
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B SER* 3.2 28.4 - - - -
268B GLU* 4.6 2.6 + - - +
269B ASP* 2.9 31.0 + - - +
272B TYR* 3.8 10.2 - - - -
274B TYR* 3.9 12.6 - - - +
318B THR* 1.3 86.9 + - - +
320B HIS* 1.3 74.8 + - - +
321B GLY 2.9 22.5 + - - +
323B LEU 3.2 13.9 - - - +
324B VAL* 4.1 7.9 - - + -
325B TYR* 4.4 0.9 - - - -
411B GLN* 5.0 2.6 + - - -
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Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR* 4.4 12.1 - - + +
319B ASN* 1.3 78.9 + - - +
321B GLY* 1.3 64.7 + - - +
322B SER 3.4 0.2 + - - -
323B LEU* 2.9 28.7 + - + +
325B TYR* 3.6 35.4 - + + +
369B GLU* 3.1 29.8 + - + -
370B GLU* 4.4 12.8 + - + +
372B PHE* 4.7 6.8 - + - -
389B LYS* 6.2 1.7 - - + +
411B GLN* 4.9 5.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il